Understanding the role of individual genetic background in his/her susceptibility to cancer, disease progression, and response to therapy is an important component of cancer research. Single nucleotide polymorphisms (SNPs) represent an abundant and useful source of genetic markers to understand complex diseases. We have characterized variants in the estrogen receptor gene (ESR1) and genotyped these variants in a cohort of breast cancer patients. The results show that a haplotype generated by several polymorphisms in this gene is associated with a reduced risk of breast cancer. In addition, we are characterizing variants in the ESR2 and progesterone receptor genes. While variants in these genes were not found to be associated with breast cancer, they may be relevant to other hormone responsive cancers. The tripartite motif-containing 5 (TRIM5) gene represents a newly described protein involved in the protection of cells from viral infection. We have sequenced the TRIM5 gene in a large collection of normal individuals as well as patients at risk for HIV-1 infection. We find a large number of non-synonymous variants in the gene, suggesting that these variants have been selected for and confer some protection to disease. In addition, the gene is conserved only in primates and is not found in the genome of the mouse, rat or dog. Evidence also shows that there is considerable variation in the gene in other primate species.